Pangea Tools Used to Design DNA Expression Chips for Hoechst Marion Roussel
Pangea Systems, Inc. (Oakland, CA) announced last month that its computational tools are being used by Hoechst Marion Roussel (HMS) and the Hoechst-ARIAD Genomics Center (a joint venture of Hoechst Marion Roussel and ARIAD Pharmaceuticals) to design custom gene expression chips from full length gene sequences and clustered gene fragments, called expressed sequence tags (ESTs), identified by HMS.
"ESTs allow researchers to discover what genes are being expressed, plus note the differences between ‘disease' genes and normal genes" explained John Burke, a research fellow at Pangea.
The new chips will enable Hoechst Marion Roussel to study gene families of potential therapeutic interest and validate their usefulness as drug targets. "Pangea's software is particularly valuable because it allows us to automatically integrate information from our compiled internal databases into designs for the manufacture of gene expression chips," said Rich Hamer, head of Hoechst Marion Roussel's Global Bioinformatics Group. "With the help of Pangea's tools, we were able to significantly accelerate our internal chip design process."
"This relationship between Pangea and Hoechst Marion Roussel illustrates how Pangea is closing the gap between genome sequencing efforts and drug target validation," said John Couch, chief executive officer of Pangea. He noted that the Hoechst-Ariad Genomics Center had previously licensed Pangea's EST Clustering and Alignment tools for use in the company's bioinformatics programs.
Pangea's chip design tools uniquely automate the identification and selection of gene sequences for incorporation into in custom DNA expression chips, rapidly producing error-free sequence sets in the appropriate format for chip manufacture. As a result, sequence selection and chip design efforts that previously required weeks to months of hand labor can be accomplished automatically in hours with greatly improved accuracy.
"Pangea's chip design software amplifies the gains that EST Clustering and Alignment tools provide," added Couch. "One component of the Pangea chip design tools automatically segregates and classifies gene isoforms and polymorphisms that may be linked to disease. The Pangea tools automatically identify optimal regions for chip design, and output the results into the input format developed by the leading chip manufacturer, Affymetrix."
Bridging the Gap between Old and New
New computational tools are essential as gene discovery and linkage to disease and treatment evolve. "The entire pharmaceutical industry is moving from sequence-based to array-based systems, both for gene discovery and for assaying the effects of drugs on genes," said Burke. "Our technology bridges the gap between sequences and chips. Companies are putting millions of dollars into EST databases or databases of their own generated from tissue samples. Now they're faced with new expression technology and they naturally don't want to lose their knowledge base. This is a serious, immediate problem for our industry. The bottom line is with our computational tools companies can translate older knowledge into new-paradigm knowledge."
"The main challenge for Pangea—and the genomics industry as a whole—is to get knowledge to the clinic, get drugs into development," Burke added. "Our computational tools help industry assay new genes in addition to discovering them. That's pretty important. We have two chip collaborations in place—the Hoechst deal plus one with Roche BioScience (Palo Alto, CA). Before Roche began using our software it took them several months to produce chips. After we got the software working, the project was done in two days."
For more information: John Burke, Research Fellow, Pangea Systems, Inc., 1999 Harrison St., Suite 1100, Oakland, CA 94612. Tel: 510-628-0100. Email: jburke@pangeasystems.com.
By Angelo DePalma